Strategies for Extending Metabolomics Studies with Stable Isotope Labelling and Fluxomics

Abstract

This is a perspective from the peer session on stable isotope labelling and fluxomics at the Australian & New Zealand Metabolomics Conference (ANZMET) held from 30 March to 1 April 2016 at La Trobe University, Melbourne, Australia. This report summarizes the key points raised in the peer session which focused on the advantages of using stable isotopes in modern metabolomics and the challenges in conducting flux analyses. The session highlighted the utility of stable isotope labelling in generating reference standards for metabolite identification, absolute quantification, and in the measurement of the dynamic activity of metabolic pathways. The advantages and disadvantages of different approaches of fluxomics analyses including flux balance analysis, metabolic flux analysis and kinetic flux profiling were also discussed along with the use of stable isotope labelling in in vivo dynamic metabolomics. A number of crucial technical considerations for designing experiments and analyzing data with stable isotope labelling were discussed which included replication, instrumentation, methods of labelling, tracer dilution and data analysis. This report reflects the current viewpoint on the use of stable isotope labelling in metabolomics experiments, identifying it as a great tool with the potential to improve biological interpretation of metabolomics data in a number of ways.

Direct and indirect approaches to identify drug modes of action

“…An alternative approach is to use selected reaction monitoring (SRM) methods, whereby the mass spectrometer is set to only select and record specific precursor/product ion combinations from the unfractionated complex mixture, greatly increasing detection sensitivity as the majority of a sample can then be rejected and ignored. The use of stable isotope‐labeled (commonly deuterium, 15 N or 13 C) metabolites can also be highly informative in focused analyses, as they allow the analyst to follow metabolic flux from a given metabolite and verify changes detected in global analyses.…”

Discovery and Validation of Clinical Biomarkers of Cancer: A Review Combining Metabolomics and Proteomics

“…When used in the context of biomarker discovery and verification, stable isotope labeling can be used to quantify the biomarkers of interest and provide mechanistic insight into the biochemistry of the cancer cells. This approach usually works by utilizing nutrients enriched with stable isotopes of atoms that occur naturally in biomolecules (such as 2 H, 13 C, 15 N, and 34 S) and performing labeling experiments over a time course to observe the dynamic nature of metabolism . Using this approach, it has been shown that compared to normal cells, cancer cells express a different isoform of the glycolytic enzyme pyruvate kinase (M2), which is associated with the accumulation of phosphoenolpyruvate, 3‐phosphoglycerate, and serine .…”

Omics in Weed Science: A Perspective from Genomics, Transcriptomics, and Metabolomics Approaches

“…Quantitation of metabolic fluxes through each reaction within a network can only be estimated indirectly with the help of isotopically labeled metabolic tracers (Gaudin et al 2014;Gleixner et al 1998;Sauer 2006). Fluxomics studies such as stable isotoperesolved metabolomics (SIRM) are emerging as powerful strategies used to measure fluxes in complex interconnected metabolic networks (Kikuchi et al 2004;Maroli et al 2016;Srivastava et al 2016). In weed science, only a couple of studies have used fluxbased omics studies to examine competitive physiology (Maroli et al 2016;Miyagi et al 2011).…”